Multiple sequence alignment - TraesCS2B01G139000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G139000 chr2B 100.000 5759 0 0 986 6744 105914005 105908247 0.000000e+00 10635.0
1 TraesCS2B01G139000 chr2B 100.000 449 0 0 1 449 105914990 105914542 0.000000e+00 830.0
2 TraesCS2B01G139000 chr2D 93.200 2250 98 22 4438 6661 69506216 69503996 0.000000e+00 3256.0
3 TraesCS2B01G139000 chr2D 92.024 1329 69 15 3027 4340 69507551 69506245 0.000000e+00 1832.0
4 TraesCS2B01G139000 chr2D 94.975 1015 47 3 1491 2502 69509244 69508231 0.000000e+00 1589.0
5 TraesCS2B01G139000 chr2D 94.807 597 17 8 2432 3022 69508230 69507642 0.000000e+00 918.0
6 TraesCS2B01G139000 chr2D 85.345 464 30 16 1 445 69510360 69509916 4.800000e-121 446.0
7 TraesCS2B01G139000 chr2D 100.000 37 0 0 6708 6744 69503986 69503950 1.210000e-07 69.4
8 TraesCS2B01G139000 chr2D 94.872 39 2 0 4387 4425 69506245 69506207 2.030000e-05 62.1
9 TraesCS2B01G139000 chr2A 94.017 1638 65 25 4534 6150 69326629 69325004 0.000000e+00 2451.0
10 TraesCS2B01G139000 chr2A 91.629 1529 69 23 989 2501 69331070 69329585 0.000000e+00 2060.0
11 TraesCS2B01G139000 chr2A 91.892 1184 60 14 2950 4122 69328894 69327736 0.000000e+00 1622.0
12 TraesCS2B01G139000 chr2A 90.803 598 39 11 6076 6661 69325014 69324421 0.000000e+00 785.0
13 TraesCS2B01G139000 chr2A 93.398 515 23 4 2431 2944 69329584 69329080 0.000000e+00 752.0
14 TraesCS2B01G139000 chr2A 88.406 414 21 4 4125 4537 69327097 69326710 2.200000e-129 473.0
15 TraesCS2B01G139000 chr2A 91.710 193 3 4 151 337 69331731 69331546 8.680000e-64 255.0
16 TraesCS2B01G139000 chr4D 81.051 723 118 13 1509 2226 173572943 173573651 5.910000e-155 558.0
17 TraesCS2B01G139000 chr4D 89.941 169 16 1 1235 1402 173572708 173572876 4.100000e-52 217.0
18 TraesCS2B01G139000 chr4A 80.632 728 113 16 1509 2229 227093922 227093216 7.700000e-149 538.0
19 TraesCS2B01G139000 chr4A 91.083 157 13 1 1247 1402 227094145 227093989 1.910000e-50 211.0
20 TraesCS2B01G139000 chr4B 79.890 726 127 13 1509 2229 246319269 246318558 1.300000e-141 514.0
21 TraesCS2B01G139000 chr4B 91.720 157 12 1 1247 1402 246319492 246319336 4.100000e-52 217.0
22 TraesCS2B01G139000 chr7B 89.017 173 13 1 2445 2617 628988101 628987935 6.850000e-50 209.0
23 TraesCS2B01G139000 chr3D 95.000 40 2 0 4186 4225 85445186 85445225 5.650000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G139000 chr2B 105908247 105914990 6743 True 5732.500000 10635 100.000000 1 6744 2 chr2B.!!$R1 6743
1 TraesCS2B01G139000 chr2D 69503950 69510360 6410 True 1167.500000 3256 93.603286 1 6744 7 chr2D.!!$R1 6743
2 TraesCS2B01G139000 chr2A 69324421 69331731 7310 True 1199.714286 2451 91.693571 151 6661 7 chr2A.!!$R1 6510
3 TraesCS2B01G139000 chr4D 173572708 173573651 943 False 387.500000 558 85.496000 1235 2226 2 chr4D.!!$F1 991
4 TraesCS2B01G139000 chr4A 227093216 227094145 929 True 374.500000 538 85.857500 1247 2229 2 chr4A.!!$R1 982
5 TraesCS2B01G139000 chr4B 246318558 246319492 934 True 365.500000 514 85.805000 1247 2229 2 chr4B.!!$R1 982

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
143 147 0.177141 TATAACTGTCCTGCGTGGGC 59.823 55.000 0.00 0.00 41.87 5.36 F
145 149 0.901114 TAACTGTCCTGCGTGGGCTA 60.901 55.000 1.93 0.00 42.07 3.93 F
1895 2369 0.532862 CTGACCGAGGTGTTTGTGCT 60.533 55.000 0.00 0.00 0.00 4.40 F
1943 2417 1.001641 GCTGTCAGGGTTGGAGCAT 60.002 57.895 1.14 0.00 33.15 3.79 F
2366 2840 1.005630 GCAGGTCTCGTGCAAGACT 60.006 57.895 16.19 2.41 44.21 3.24 F
3944 4768 0.462581 GCGATCCATCAAGTCTGCCA 60.463 55.000 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 2369 0.108186 CATAGCACTTGACCTGCGGA 60.108 55.000 0.00 0.00 39.79 5.54 R
1991 2465 0.243907 CACCGTCGTCATCCAAGAGT 59.756 55.000 0.00 0.00 0.00 3.24 R
2938 3490 2.353704 AGGCACTGATTTCGTGATTCGA 60.354 45.455 0.00 0.00 42.49 3.71 R
3627 4451 4.831710 AGTTAAAACTCCGTACAGAGGACT 59.168 41.667 10.79 4.00 38.26 3.85 R
4192 5658 1.992233 ATAGCAACGCACGGGCATTG 61.992 55.000 15.24 15.24 45.48 2.82 R
5805 7422 0.253347 TCTCCCCAGCTTCCAGGAAT 60.253 55.000 1.09 0.00 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.717113 GGCGGTAACAAACAAAATCGC 59.283 47.619 0.00 0.00 40.97 4.58
28 29 1.380771 GCGGTAACAAACAAAATCGCG 59.619 47.619 0.00 0.00 32.93 5.87
29 30 2.906153 CGGTAACAAACAAAATCGCGA 58.094 42.857 13.09 13.09 0.00 5.87
30 31 3.484683 CGGTAACAAACAAAATCGCGAT 58.515 40.909 17.62 17.62 0.00 4.58
31 32 4.639959 CGGTAACAAACAAAATCGCGATA 58.360 39.130 24.00 0.00 0.00 2.92
89 93 9.593134 TTGCTACATTTTGTTTGTCAATAACTT 57.407 25.926 0.00 0.00 35.84 2.66
90 94 9.029243 TGCTACATTTTGTTTGTCAATAACTTG 57.971 29.630 0.00 0.00 35.84 3.16
116 120 6.855763 TTGTTATGATGCATTTCCCTCTTT 57.144 33.333 0.00 0.00 0.00 2.52
117 121 6.855763 TGTTATGATGCATTTCCCTCTTTT 57.144 33.333 0.00 0.00 0.00 2.27
119 123 8.359875 TGTTATGATGCATTTCCCTCTTTTTA 57.640 30.769 0.00 0.00 0.00 1.52
120 124 8.980596 TGTTATGATGCATTTCCCTCTTTTTAT 58.019 29.630 0.00 0.00 0.00 1.40
122 126 9.820725 TTATGATGCATTTCCCTCTTTTTATTG 57.179 29.630 0.00 0.00 0.00 1.90
123 127 7.479352 TGATGCATTTCCCTCTTTTTATTGA 57.521 32.000 0.00 0.00 0.00 2.57
125 129 9.199645 TGATGCATTTCCCTCTTTTTATTGATA 57.800 29.630 0.00 0.00 0.00 2.15
134 138 9.847224 TCCCTCTTTTTATTGATATAACTGTCC 57.153 33.333 0.00 0.00 0.00 4.02
135 139 9.853177 CCCTCTTTTTATTGATATAACTGTCCT 57.147 33.333 0.00 0.00 0.00 3.85
139 143 8.500753 TTTTTATTGATATAACTGTCCTGCGT 57.499 30.769 0.00 0.00 0.00 5.24
142 146 2.102420 TGATATAACTGTCCTGCGTGGG 59.898 50.000 0.00 0.00 36.20 4.61
143 147 0.177141 TATAACTGTCCTGCGTGGGC 59.823 55.000 0.00 0.00 41.87 5.36
144 148 1.553690 ATAACTGTCCTGCGTGGGCT 61.554 55.000 1.93 0.00 42.07 5.19
145 149 0.901114 TAACTGTCCTGCGTGGGCTA 60.901 55.000 1.93 0.00 42.07 3.93
146 150 2.125512 CTGTCCTGCGTGGGCTAC 60.126 66.667 1.93 0.00 42.07 3.58
205 209 4.305524 AGGAAACATCCATCCAGAGAGAT 58.694 43.478 0.00 0.00 38.23 2.75
206 210 4.102838 AGGAAACATCCATCCAGAGAGATG 59.897 45.833 7.71 7.71 42.79 2.90
256 266 3.662759 AAACCAGAACCAGAACCAGAA 57.337 42.857 0.00 0.00 0.00 3.02
257 267 2.640316 ACCAGAACCAGAACCAGAAC 57.360 50.000 0.00 0.00 0.00 3.01
258 268 1.143073 ACCAGAACCAGAACCAGAACC 59.857 52.381 0.00 0.00 0.00 3.62
259 269 1.142870 CCAGAACCAGAACCAGAACCA 59.857 52.381 0.00 0.00 0.00 3.67
260 270 2.422803 CCAGAACCAGAACCAGAACCAA 60.423 50.000 0.00 0.00 0.00 3.67
261 271 3.287222 CAGAACCAGAACCAGAACCAAA 58.713 45.455 0.00 0.00 0.00 3.28
1168 1514 3.068691 CCGAGAAGGACGGGCAGA 61.069 66.667 0.00 0.00 45.65 4.26
1169 1515 2.182030 CGAGAAGGACGGGCAGAC 59.818 66.667 0.00 0.00 0.00 3.51
1170 1516 2.182030 GAGAAGGACGGGCAGACG 59.818 66.667 0.00 0.00 40.31 4.18
1226 1572 3.272334 GTCATCGCGGCATGGTCC 61.272 66.667 6.13 0.00 0.00 4.46
1227 1573 4.545706 TCATCGCGGCATGGTCCC 62.546 66.667 6.13 0.00 0.00 4.46
1415 1761 3.866582 CCCCCACCATCTCCGAGC 61.867 72.222 0.00 0.00 0.00 5.03
1416 1762 2.765807 CCCCACCATCTCCGAGCT 60.766 66.667 0.00 0.00 0.00 4.09
1417 1763 2.801631 CCCCACCATCTCCGAGCTC 61.802 68.421 2.73 2.73 0.00 4.09
1418 1764 2.801631 CCCACCATCTCCGAGCTCC 61.802 68.421 8.47 0.00 0.00 4.70
1419 1765 2.801631 CCACCATCTCCGAGCTCCC 61.802 68.421 8.47 0.00 0.00 4.30
1420 1766 2.444895 ACCATCTCCGAGCTCCCC 60.445 66.667 8.47 0.00 0.00 4.81
1421 1767 3.237741 CCATCTCCGAGCTCCCCC 61.238 72.222 8.47 0.00 0.00 5.40
1687 2150 1.460504 ACGTCATGAAGCTCTACGGA 58.539 50.000 8.68 0.00 37.86 4.69
1841 2307 6.683974 ACAGCCACATAGTGACAAATTATC 57.316 37.500 0.00 0.00 35.23 1.75
1842 2308 6.179756 ACAGCCACATAGTGACAAATTATCA 58.820 36.000 0.00 0.00 35.23 2.15
1843 2309 6.094048 ACAGCCACATAGTGACAAATTATCAC 59.906 38.462 12.71 12.71 45.70 3.06
1855 2322 8.702438 GTGACAAATTATCACTTCAAAATGTGG 58.298 33.333 13.15 0.00 42.68 4.17
1857 2324 8.816640 ACAAATTATCACTTCAAAATGTGGTC 57.183 30.769 0.00 0.00 35.15 4.02
1860 2327 3.988379 TCACTTCAAAATGTGGTCTGC 57.012 42.857 0.00 0.00 35.15 4.26
1864 2331 3.067180 ACTTCAAAATGTGGTCTGCTGTG 59.933 43.478 0.00 0.00 0.00 3.66
1895 2369 0.532862 CTGACCGAGGTGTTTGTGCT 60.533 55.000 0.00 0.00 0.00 4.40
1943 2417 1.001641 GCTGTCAGGGTTGGAGCAT 60.002 57.895 1.14 0.00 33.15 3.79
1991 2465 2.034685 CGACATCAAGGGCTCGAATCTA 59.965 50.000 0.00 0.00 0.00 1.98
2042 2516 1.371558 GGACTTTGGTCTGGCGTCT 59.628 57.895 0.00 0.00 41.82 4.18
2081 2555 1.374252 GCAACCGATGACCAGTCGT 60.374 57.895 0.00 0.00 37.39 4.34
2093 2567 2.027605 AGTCGTGTGGTGACGCTG 59.972 61.111 0.00 0.00 41.24 5.18
2270 2744 9.575868 TTCCCACAAATGTTACTAAAGTTGATA 57.424 29.630 0.00 0.00 0.00 2.15
2312 2786 4.201763 GCTGAAGTACTGTTCATAGCTTGC 60.202 45.833 0.00 0.00 35.88 4.01
2333 2807 2.027007 CCAACCATTCCATGCAAACCAT 60.027 45.455 0.00 0.00 33.39 3.55
2366 2840 1.005630 GCAGGTCTCGTGCAAGACT 60.006 57.895 16.19 2.41 44.21 3.24
2451 2926 2.432444 TGTTGTTCTTTATCAGGGGCG 58.568 47.619 0.00 0.00 0.00 6.13
2812 3364 4.228666 TGCCCTTTGGTCCTATAAAAGCTA 59.771 41.667 0.00 0.00 31.03 3.32
2856 3408 6.646267 AGTCGAAATTTTGGCTACCAGTATA 58.354 36.000 10.94 0.00 33.81 1.47
2947 3499 3.430609 GCTGAAGCATATCGAATCACG 57.569 47.619 0.00 0.00 41.59 4.35
3004 3736 9.955208 TGCAGTTCATATTTGTCATGAATAATC 57.045 29.630 0.00 0.00 42.63 1.75
3128 3948 7.279615 TCATGTCTTCTTTTCAGGTAGAACAA 58.720 34.615 0.00 0.00 35.56 2.83
3182 4002 5.343249 CCCGCTGAAGAATATTGGAAAAAG 58.657 41.667 0.00 0.00 0.00 2.27
3308 4128 6.122277 TGAAACACTCCTATCAATTGATCCC 58.878 40.000 23.95 4.04 36.05 3.85
3627 4451 6.756542 CACATTGAGATCACGGTATCTTGTTA 59.243 38.462 0.00 0.00 36.33 2.41
3628 4452 6.980978 ACATTGAGATCACGGTATCTTGTTAG 59.019 38.462 0.00 0.00 36.33 2.34
3639 4463 5.503683 CGGTATCTTGTTAGTCCTCTGTACG 60.504 48.000 0.00 0.00 0.00 3.67
3646 4470 4.586001 TGTTAGTCCTCTGTACGGAGTTTT 59.414 41.667 26.35 15.01 37.78 2.43
3661 4485 7.019774 ACGGAGTTTTAACTTTTAGGTTCAC 57.980 36.000 0.00 0.00 37.78 3.18
3685 4509 3.480470 AGGTCCATGAAATTATGCTCGG 58.520 45.455 0.00 0.00 0.00 4.63
3859 4683 2.862541 TGCTGCTCCTTGTTGTTACAT 58.137 42.857 0.00 0.00 33.44 2.29
3870 4694 5.694910 CCTTGTTGTTACATCGTACTTGACT 59.305 40.000 0.00 0.00 33.44 3.41
3944 4768 0.462581 GCGATCCATCAAGTCTGCCA 60.463 55.000 0.00 0.00 0.00 4.92
3980 4804 3.504863 CAAAGAGATGGATGCAAAACGG 58.495 45.455 0.00 0.00 0.00 4.44
4023 4847 5.070685 GGTTTGTCATCCTAACACTCCTTT 58.929 41.667 0.00 0.00 0.00 3.11
4060 4884 6.108015 AGTTGTGTTGATTTTCTGCATTTGT 58.892 32.000 0.00 0.00 0.00 2.83
4112 4942 7.550906 GTCATTTAAGCTCTTCACAACCTAGAT 59.449 37.037 0.00 0.00 0.00 1.98
4123 5589 8.590204 TCTTCACAACCTAGATATGTAAACACA 58.410 33.333 0.00 0.00 0.00 3.72
4189 5655 2.588620 TGGGCCGTTGAAACAAACTAT 58.411 42.857 0.00 0.00 0.00 2.12
4192 5658 3.561503 GGCCGTTGAAACAAACTATCAC 58.438 45.455 0.00 0.00 0.00 3.06
4195 5661 5.219633 GCCGTTGAAACAAACTATCACAAT 58.780 37.500 0.00 0.00 0.00 2.71
4297 5766 1.330521 CAACACTGCACTTGCGTAACT 59.669 47.619 0.00 0.00 45.83 2.24
4298 5767 0.937304 ACACTGCACTTGCGTAACTG 59.063 50.000 0.00 0.00 45.83 3.16
4356 5825 3.825143 GCATAGCCATGGTTGGATTTT 57.175 42.857 14.67 0.00 46.92 1.82
4357 5826 3.460103 GCATAGCCATGGTTGGATTTTG 58.540 45.455 14.67 1.93 46.92 2.44
4358 5827 3.132646 GCATAGCCATGGTTGGATTTTGA 59.867 43.478 14.67 0.00 46.92 2.69
4359 5828 4.382901 GCATAGCCATGGTTGGATTTTGAA 60.383 41.667 14.67 0.00 46.92 2.69
4360 5829 5.732633 CATAGCCATGGTTGGATTTTGAAA 58.267 37.500 14.67 0.00 46.92 2.69
4361 5830 4.914177 AGCCATGGTTGGATTTTGAAAT 57.086 36.364 14.67 0.00 46.92 2.17
4362 5831 5.245584 AGCCATGGTTGGATTTTGAAATT 57.754 34.783 14.67 0.00 46.92 1.82
4363 5832 5.633117 AGCCATGGTTGGATTTTGAAATTT 58.367 33.333 14.67 0.00 46.92 1.82
4364 5833 6.069994 AGCCATGGTTGGATTTTGAAATTTT 58.930 32.000 14.67 0.00 46.92 1.82
4365 5834 7.230027 AGCCATGGTTGGATTTTGAAATTTTA 58.770 30.769 14.67 0.00 46.92 1.52
4366 5835 7.723172 AGCCATGGTTGGATTTTGAAATTTTAA 59.277 29.630 14.67 0.00 46.92 1.52
4367 5836 8.355913 GCCATGGTTGGATTTTGAAATTTTAAA 58.644 29.630 14.67 4.15 46.92 1.52
4368 5837 9.896263 CCATGGTTGGATTTTGAAATTTTAAAG 57.104 29.630 2.57 0.00 46.92 1.85
4426 5939 3.878667 GGGGATTGGGGAGGAGCG 61.879 72.222 0.00 0.00 0.00 5.03
4427 5940 3.878667 GGGATTGGGGAGGAGCGG 61.879 72.222 0.00 0.00 0.00 5.52
4428 5941 2.768344 GGATTGGGGAGGAGCGGA 60.768 66.667 0.00 0.00 0.00 5.54
4429 5942 2.506472 GATTGGGGAGGAGCGGAC 59.494 66.667 0.00 0.00 0.00 4.79
4430 5943 2.285368 ATTGGGGAGGAGCGGACA 60.285 61.111 0.00 0.00 0.00 4.02
4431 5944 2.595009 GATTGGGGAGGAGCGGACAC 62.595 65.000 0.00 0.00 0.00 3.67
4434 5947 3.003763 GGGAGGAGCGGACACCTT 61.004 66.667 0.00 0.00 36.95 3.50
4435 5948 2.593956 GGGAGGAGCGGACACCTTT 61.594 63.158 0.00 0.00 36.95 3.11
4436 5949 1.079057 GGAGGAGCGGACACCTTTC 60.079 63.158 0.00 0.00 36.95 2.62
4437 5950 1.545706 GGAGGAGCGGACACCTTTCT 61.546 60.000 0.00 0.00 36.95 2.52
4438 5951 0.390472 GAGGAGCGGACACCTTTCTG 60.390 60.000 0.00 0.00 36.95 3.02
4439 5952 1.376037 GGAGCGGACACCTTTCTGG 60.376 63.158 0.00 0.00 42.93 3.86
4440 5953 1.376037 GAGCGGACACCTTTCTGGG 60.376 63.158 0.00 0.00 41.11 4.45
4442 5955 2.890766 GCGGACACCTTTCTGGGGA 61.891 63.158 0.00 0.00 43.63 4.81
4443 5956 1.296715 CGGACACCTTTCTGGGGAG 59.703 63.158 0.00 0.00 43.63 4.30
4444 5957 1.685820 GGACACCTTTCTGGGGAGG 59.314 63.158 0.00 0.00 43.63 4.30
4445 5958 0.840722 GGACACCTTTCTGGGGAGGA 60.841 60.000 0.00 0.00 43.63 3.71
4446 5959 0.615850 GACACCTTTCTGGGGAGGAG 59.384 60.000 0.00 0.00 43.63 3.69
4447 5960 1.301293 CACCTTTCTGGGGAGGAGC 59.699 63.158 0.00 0.00 43.63 4.70
4512 6025 3.149436 TGCTGCGGAAAAGAATAATGC 57.851 42.857 0.00 0.00 0.00 3.56
4558 6155 5.047802 ACTTTCCTATGCAAAACATGAGTGG 60.048 40.000 0.00 0.00 40.06 4.00
4561 6158 2.443887 ATGCAAAACATGAGTGGCAC 57.556 45.000 10.29 10.29 37.70 5.01
4569 6166 3.612247 ATGAGTGGCACGGTGGCTC 62.612 63.158 30.89 27.34 44.10 4.70
4576 6173 3.041940 CACGGTGGCTCGTTGGAC 61.042 66.667 0.00 0.00 41.86 4.02
4597 6194 0.760945 AGAAGGGATCTGGTAGGCCG 60.761 60.000 0.00 0.00 36.88 6.13
4657 6254 3.055719 CATCGCCACCACCACCAC 61.056 66.667 0.00 0.00 0.00 4.16
4658 6255 4.344865 ATCGCCACCACCACCACC 62.345 66.667 0.00 0.00 0.00 4.61
4662 6259 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
4806 6406 9.880157 AGTATTCTAAAATCTAGTTTGCCGTAA 57.120 29.630 0.00 0.00 0.00 3.18
4827 6431 2.170187 AGAGCCTACTTCTGCAGAATGG 59.830 50.000 28.57 27.02 35.86 3.16
4848 6452 5.789521 TGGTTCGATGAACTTGATAACAGA 58.210 37.500 9.32 0.00 41.70 3.41
4857 6461 9.495754 GATGAACTTGATAACAGAAAAGCATAC 57.504 33.333 0.00 0.00 0.00 2.39
4887 6491 3.538379 TGTACAGCACAGCAGGATG 57.462 52.632 0.00 0.00 32.52 3.51
4943 6547 2.354805 GGTAACTTCAGTGGGTGCTAGG 60.355 54.545 0.00 0.00 0.00 3.02
5032 6637 2.648059 CTGGGAGCTTGTTGGGAATAG 58.352 52.381 0.00 0.00 0.00 1.73
5112 6717 9.905713 TCTGGTGTATATTTAATGCTTCTTTCT 57.094 29.630 0.00 0.00 0.00 2.52
5158 6764 1.971357 TCTCCACCTCTTGACCTTGTC 59.029 52.381 0.00 0.00 0.00 3.18
5343 6949 2.422276 ATGCCGAACTTCAAGCAAAC 57.578 45.000 7.39 0.00 38.99 2.93
5349 6955 3.120199 CCGAACTTCAAGCAAACATCGAT 60.120 43.478 0.00 0.00 0.00 3.59
5393 7009 3.440173 CCCTACAAGTTACAGTTGCATGG 59.560 47.826 0.00 0.00 31.85 3.66
5418 7034 1.098712 TTTTTCCGCTTGCCGTGTCT 61.099 50.000 0.00 0.00 34.38 3.41
5425 7041 1.227999 GCTTGCCGTGTCTGCTGTTA 61.228 55.000 0.00 0.00 0.00 2.41
5596 7213 1.856873 ATTTGAGCCCCCAGACCCA 60.857 57.895 0.00 0.00 0.00 4.51
5635 7252 0.963962 TTCCTTACGACAAGACCGCT 59.036 50.000 0.00 0.00 0.00 5.52
5698 7315 3.839293 CAACCAGAAACGGAAACACAAA 58.161 40.909 0.00 0.00 0.00 2.83
5707 7324 2.139917 CGGAAACACAAATCTGGACGA 58.860 47.619 0.00 0.00 0.00 4.20
5805 7422 2.224549 CGGACAATTTACTCGGCAACAA 59.775 45.455 0.00 0.00 0.00 2.83
5843 7460 5.477291 GGGAGATCTGATTATACGACCAAGA 59.523 44.000 0.00 0.00 0.00 3.02
5863 7480 4.479619 AGACAAGCAGCGATGAATTTTTC 58.520 39.130 4.02 0.00 0.00 2.29
6176 7870 6.154363 TCCAGCTTTATGTTTTCCCTTTATGG 59.846 38.462 0.00 0.00 0.00 2.74
6211 7907 9.685276 TGTAGATTCAGACAATTTGGACATTAT 57.315 29.630 0.78 0.00 0.00 1.28
6294 7992 5.438761 ACAGTTTCAACTTCTGGCAATAC 57.561 39.130 0.00 0.00 37.08 1.89
6295 7993 4.887071 ACAGTTTCAACTTCTGGCAATACA 59.113 37.500 0.00 0.00 37.08 2.29
6435 8133 1.452833 GTGGCCCTTCCTGCAGATC 60.453 63.158 17.39 0.00 35.26 2.75
6451 8149 0.038709 GATCTCATCTTCCCGGAGCG 60.039 60.000 0.73 0.00 0.00 5.03
6597 8299 6.308566 ACCAGAGGAGGATGATAAGTACTAC 58.691 44.000 0.00 0.00 0.00 2.73
6601 8303 8.598916 CAGAGGAGGATGATAAGTACTACTAGA 58.401 40.741 0.00 0.00 0.00 2.43
6615 8317 7.733969 AGTACTACTAGATCAGATTCGGTACA 58.266 38.462 0.00 0.00 0.00 2.90
6637 8339 5.920273 ACAAGCATTACGGTTCAAAATTCAG 59.080 36.000 0.00 0.00 31.36 3.02
6641 8343 5.569059 GCATTACGGTTCAAAATTCAGACAG 59.431 40.000 0.00 0.00 0.00 3.51
6643 8345 2.293399 ACGGTTCAAAATTCAGACAGCC 59.707 45.455 0.00 0.00 0.00 4.85
6661 8363 4.740822 GTTGGCGGGCATGGGACT 62.741 66.667 4.64 0.00 0.00 3.85
6667 8369 2.763215 GGGCATGGGACTGGTGAA 59.237 61.111 0.00 0.00 0.00 3.18
6668 8370 1.076549 GGGCATGGGACTGGTGAAA 59.923 57.895 0.00 0.00 0.00 2.69
6669 8371 0.967380 GGGCATGGGACTGGTGAAAG 60.967 60.000 0.00 0.00 0.00 2.62
6670 8372 0.251341 GGCATGGGACTGGTGAAAGT 60.251 55.000 0.00 0.00 0.00 2.66
6671 8373 0.883833 GCATGGGACTGGTGAAAGTG 59.116 55.000 0.00 0.00 0.00 3.16
6672 8374 1.545428 GCATGGGACTGGTGAAAGTGA 60.545 52.381 0.00 0.00 0.00 3.41
6673 8375 2.430465 CATGGGACTGGTGAAAGTGAG 58.570 52.381 0.00 0.00 0.00 3.51
6674 8376 1.801242 TGGGACTGGTGAAAGTGAGA 58.199 50.000 0.00 0.00 0.00 3.27
6675 8377 1.694150 TGGGACTGGTGAAAGTGAGAG 59.306 52.381 0.00 0.00 0.00 3.20
6676 8378 1.002544 GGGACTGGTGAAAGTGAGAGG 59.997 57.143 0.00 0.00 0.00 3.69
6677 8379 1.971357 GGACTGGTGAAAGTGAGAGGA 59.029 52.381 0.00 0.00 0.00 3.71
6678 8380 2.028567 GGACTGGTGAAAGTGAGAGGAG 60.029 54.545 0.00 0.00 0.00 3.69
6679 8381 2.894126 GACTGGTGAAAGTGAGAGGAGA 59.106 50.000 0.00 0.00 0.00 3.71
6680 8382 3.309296 ACTGGTGAAAGTGAGAGGAGAA 58.691 45.455 0.00 0.00 0.00 2.87
6681 8383 3.906846 ACTGGTGAAAGTGAGAGGAGAAT 59.093 43.478 0.00 0.00 0.00 2.40
6682 8384 4.349342 ACTGGTGAAAGTGAGAGGAGAATT 59.651 41.667 0.00 0.00 0.00 2.17
6683 8385 5.163152 ACTGGTGAAAGTGAGAGGAGAATTT 60.163 40.000 0.00 0.00 0.00 1.82
6684 8386 5.308825 TGGTGAAAGTGAGAGGAGAATTTC 58.691 41.667 0.00 0.00 0.00 2.17
6685 8387 5.072329 TGGTGAAAGTGAGAGGAGAATTTCT 59.928 40.000 0.00 0.00 0.00 2.52
6686 8388 5.411053 GGTGAAAGTGAGAGGAGAATTTCTG 59.589 44.000 3.03 0.00 0.00 3.02
6687 8389 5.994668 GTGAAAGTGAGAGGAGAATTTCTGT 59.005 40.000 3.03 0.00 0.00 3.41
6688 8390 6.147000 GTGAAAGTGAGAGGAGAATTTCTGTC 59.853 42.308 3.03 0.72 0.00 3.51
6689 8391 5.815233 AAGTGAGAGGAGAATTTCTGTCA 57.185 39.130 3.03 0.00 32.05 3.58
6690 8392 6.371595 AAGTGAGAGGAGAATTTCTGTCAT 57.628 37.500 3.03 0.00 36.06 3.06
6691 8393 6.371595 AGTGAGAGGAGAATTTCTGTCATT 57.628 37.500 3.03 0.00 36.06 2.57
6692 8394 6.777782 AGTGAGAGGAGAATTTCTGTCATTT 58.222 36.000 3.03 0.00 36.06 2.32
6693 8395 7.230027 AGTGAGAGGAGAATTTCTGTCATTTT 58.770 34.615 3.03 0.00 36.06 1.82
6694 8396 7.723172 AGTGAGAGGAGAATTTCTGTCATTTTT 59.277 33.333 3.03 0.00 36.06 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.547285 TTTTCTCTTATCGCGATTTTGTTTG 57.453 32.000 28.81 11.19 0.00 2.93
42 46 7.264221 AGCAATATTTGATTATTGGTTTGCGA 58.736 30.769 3.72 0.00 43.94 5.10
63 67 9.593134 AAGTTATTGACAAACAAAATGTAGCAA 57.407 25.926 0.00 0.00 42.03 3.91
64 68 9.029243 CAAGTTATTGACAAACAAAATGTAGCA 57.971 29.630 0.00 0.00 42.03 3.49
79 83 9.190858 TGCATCATAACAAAACAAGTTATTGAC 57.809 29.630 11.83 0.00 39.46 3.18
84 88 9.202273 GGAAATGCATCATAACAAAACAAGTTA 57.798 29.630 0.00 0.00 36.06 2.24
85 89 7.173047 GGGAAATGCATCATAACAAAACAAGTT 59.827 33.333 0.00 0.00 0.00 2.66
86 90 6.650390 GGGAAATGCATCATAACAAAACAAGT 59.350 34.615 0.00 0.00 0.00 3.16
87 91 6.875195 AGGGAAATGCATCATAACAAAACAAG 59.125 34.615 0.00 0.00 0.00 3.16
89 93 6.211184 AGAGGGAAATGCATCATAACAAAACA 59.789 34.615 0.00 0.00 0.00 2.83
90 94 6.633856 AGAGGGAAATGCATCATAACAAAAC 58.366 36.000 0.00 0.00 0.00 2.43
95 99 9.822185 AATAAAAAGAGGGAAATGCATCATAAC 57.178 29.630 0.00 0.00 0.00 1.89
97 101 9.199645 TCAATAAAAAGAGGGAAATGCATCATA 57.800 29.630 0.00 0.00 0.00 2.15
109 113 9.853177 AGGACAGTTATATCAATAAAAAGAGGG 57.147 33.333 0.00 0.00 29.41 4.30
116 120 6.481976 CCACGCAGGACAGTTATATCAATAAA 59.518 38.462 0.00 0.00 41.22 1.40
117 121 5.989168 CCACGCAGGACAGTTATATCAATAA 59.011 40.000 0.00 0.00 41.22 1.40
119 123 4.380531 CCACGCAGGACAGTTATATCAAT 58.619 43.478 0.00 0.00 41.22 2.57
120 124 3.431626 CCCACGCAGGACAGTTATATCAA 60.432 47.826 0.00 0.00 41.22 2.57
122 126 2.755650 CCCACGCAGGACAGTTATATC 58.244 52.381 0.00 0.00 41.22 1.63
123 127 1.202651 GCCCACGCAGGACAGTTATAT 60.203 52.381 0.00 0.00 41.22 0.86
125 129 1.078426 GCCCACGCAGGACAGTTAT 60.078 57.895 0.00 0.00 41.22 1.89
126 130 0.901114 TAGCCCACGCAGGACAGTTA 60.901 55.000 0.00 0.00 41.22 2.24
128 132 2.603473 TAGCCCACGCAGGACAGT 60.603 61.111 0.00 0.00 41.22 3.55
129 133 2.125512 GTAGCCCACGCAGGACAG 60.126 66.667 0.00 0.00 41.22 3.51
130 134 4.063967 CGTAGCCCACGCAGGACA 62.064 66.667 0.00 0.00 45.03 4.02
139 143 0.542467 TACAGAACCACCGTAGCCCA 60.542 55.000 0.00 0.00 0.00 5.36
142 146 1.135170 GTCCTACAGAACCACCGTAGC 60.135 57.143 0.00 0.00 32.90 3.58
143 147 2.165167 TGTCCTACAGAACCACCGTAG 58.835 52.381 0.00 0.00 33.82 3.51
144 148 2.291209 TGTCCTACAGAACCACCGTA 57.709 50.000 0.00 0.00 0.00 4.02
145 149 3.136620 TGTCCTACAGAACCACCGT 57.863 52.632 0.00 0.00 0.00 4.83
206 210 2.745492 GTCTGCTCCTGCACCTGC 60.745 66.667 0.00 0.00 45.31 4.85
256 266 1.830847 GAACCCAACCGGCTTTGGT 60.831 57.895 19.48 12.99 44.16 3.67
257 267 2.570284 GGAACCCAACCGGCTTTGG 61.570 63.158 15.38 15.38 45.11 3.28
258 268 1.830408 TGGAACCCAACCGGCTTTG 60.830 57.895 0.00 0.00 33.26 2.77
259 269 1.830847 GTGGAACCCAACCGGCTTT 60.831 57.895 0.00 0.00 34.18 3.51
260 270 2.203437 GTGGAACCCAACCGGCTT 60.203 61.111 0.00 0.00 34.18 4.35
261 271 3.175710 AGTGGAACCCAACCGGCT 61.176 61.111 0.00 0.00 37.80 5.52
353 372 2.272698 GGGGTGGGGAGTAGTAAAGTT 58.727 52.381 0.00 0.00 0.00 2.66
1151 1497 3.068691 TCTGCCCGTCCTTCTCGG 61.069 66.667 0.00 0.00 46.49 4.63
1399 1745 2.765807 AGCTCGGAGATGGTGGGG 60.766 66.667 9.69 0.00 33.89 4.96
1400 1746 2.801631 GGAGCTCGGAGATGGTGGG 61.802 68.421 9.69 0.00 33.89 4.61
1401 1747 2.801631 GGGAGCTCGGAGATGGTGG 61.802 68.421 9.69 0.00 33.89 4.61
1402 1748 2.801631 GGGGAGCTCGGAGATGGTG 61.802 68.421 9.69 0.00 33.89 4.17
1403 1749 2.444895 GGGGAGCTCGGAGATGGT 60.445 66.667 9.69 0.00 33.89 3.55
1404 1750 3.237741 GGGGGAGCTCGGAGATGG 61.238 72.222 9.69 0.00 33.89 3.51
1556 2019 1.522355 CCACGATCTTGCCGCTCAT 60.522 57.895 0.00 0.00 0.00 2.90
1687 2150 2.680352 ATGCGGGAGGTGACGAGT 60.680 61.111 0.00 0.00 0.00 4.18
1841 2307 3.067180 ACAGCAGACCACATTTTGAAGTG 59.933 43.478 0.00 0.00 35.56 3.16
1842 2308 3.067180 CACAGCAGACCACATTTTGAAGT 59.933 43.478 0.00 0.00 0.00 3.01
1843 2309 3.551454 CCACAGCAGACCACATTTTGAAG 60.551 47.826 0.00 0.00 0.00 3.02
1844 2310 2.361757 CCACAGCAGACCACATTTTGAA 59.638 45.455 0.00 0.00 0.00 2.69
1846 2312 1.603678 GCCACAGCAGACCACATTTTG 60.604 52.381 0.00 0.00 39.53 2.44
1855 2322 0.179150 CTCGACTAGCCACAGCAGAC 60.179 60.000 0.00 0.00 43.56 3.51
1857 2324 0.179150 GACTCGACTAGCCACAGCAG 60.179 60.000 0.00 0.00 43.56 4.24
1860 2327 1.131504 GTCAGACTCGACTAGCCACAG 59.868 57.143 0.00 0.00 32.92 3.66
1864 2331 0.743701 TCGGTCAGACTCGACTAGCC 60.744 60.000 9.33 0.00 36.12 3.93
1895 2369 0.108186 CATAGCACTTGACCTGCGGA 60.108 55.000 0.00 0.00 39.79 5.54
1943 2417 1.152777 CACTCCCTGGTTGTGGCAA 60.153 57.895 8.01 0.00 0.00 4.52
1970 2444 1.202463 AGATTCGAGCCCTTGATGTCG 60.202 52.381 0.00 0.00 0.00 4.35
1991 2465 0.243907 CACCGTCGTCATCCAAGAGT 59.756 55.000 0.00 0.00 0.00 3.24
2042 2516 3.592059 CTTATGGTTCGGGTCGAAGAAA 58.408 45.455 2.83 0.00 46.54 2.52
2081 2555 1.068417 GTACCACAGCGTCACCACA 59.932 57.895 0.00 0.00 0.00 4.17
2270 2744 4.398988 TCAGCAAAATCACACTTGAACAGT 59.601 37.500 0.00 0.00 34.61 3.55
2312 2786 1.347050 TGGTTTGCATGGAATGGTTGG 59.653 47.619 0.00 0.00 46.86 3.77
2333 2807 4.993028 AGACCTGCCCTAAAATGTTAACA 58.007 39.130 11.41 11.41 0.00 2.41
2346 2820 2.743928 CTTGCACGAGACCTGCCC 60.744 66.667 0.00 0.00 33.36 5.36
2366 2840 6.063404 TGTATATCATTTCATCAGCAAGGCA 58.937 36.000 0.00 0.00 0.00 4.75
2451 2926 2.356227 GGGTCAATTTCTCTCTGGGTCC 60.356 54.545 0.00 0.00 0.00 4.46
2812 3364 5.124457 CGACTCCATTCTTGTCCAAAATGAT 59.876 40.000 12.42 3.54 33.22 2.45
2856 3408 7.940850 AGTATGCGGTCTAAATATTTGCAAAT 58.059 30.769 26.72 26.72 34.21 2.32
2874 3426 7.408910 TCACATGTATGATTTTCAAGTATGCG 58.591 34.615 0.00 0.00 0.00 4.73
2938 3490 2.353704 AGGCACTGATTTCGTGATTCGA 60.354 45.455 0.00 0.00 42.49 3.71
2944 3496 6.128282 ACAAAGTATTAGGCACTGATTTCGTG 60.128 38.462 0.00 0.00 41.52 4.35
2945 3497 5.938125 ACAAAGTATTAGGCACTGATTTCGT 59.062 36.000 0.00 0.00 41.52 3.85
2946 3498 6.422776 ACAAAGTATTAGGCACTGATTTCG 57.577 37.500 0.00 0.00 41.52 3.46
2947 3499 6.528072 GCAACAAAGTATTAGGCACTGATTTC 59.472 38.462 0.00 0.00 41.52 2.17
2948 3500 6.015519 TGCAACAAAGTATTAGGCACTGATTT 60.016 34.615 0.00 0.00 41.52 2.17
3037 3769 8.994500 TGTGGGGATAAAGTATTACTACATCAA 58.006 33.333 14.68 3.37 0.00 2.57
3094 3912 9.748708 CCTGAAAAGAAGACATGATTAAAAACA 57.251 29.630 0.00 0.00 0.00 2.83
3095 3913 9.750125 ACCTGAAAAGAAGACATGATTAAAAAC 57.250 29.630 0.00 0.00 0.00 2.43
3128 3948 9.357652 CCGCATAGCTTAAATATTTTATGCAAT 57.642 29.630 26.74 11.65 41.95 3.56
3512 4336 8.556213 ACAAGTTTAAACAAGTACAGAAGACA 57.444 30.769 20.06 0.00 0.00 3.41
3627 4451 4.831710 AGTTAAAACTCCGTACAGAGGACT 59.168 41.667 10.79 4.00 38.26 3.85
3628 4452 5.131594 AGTTAAAACTCCGTACAGAGGAC 57.868 43.478 10.79 2.04 38.26 3.85
3646 4470 7.319052 TGGACCTATGTGAACCTAAAAGTTA 57.681 36.000 0.00 0.00 0.00 2.24
3661 4485 5.122869 CCGAGCATAATTTCATGGACCTATG 59.877 44.000 0.00 0.00 0.00 2.23
3732 4556 5.422214 AGAATTCGGGTTCTGTCTTACAT 57.578 39.130 0.00 0.00 37.08 2.29
3820 4644 8.147642 AGCAGCAATGTAGATACTTCATAAAC 57.852 34.615 0.00 0.00 0.00 2.01
3859 4683 6.639632 AAAGGTGTAAGTAGTCAAGTACGA 57.360 37.500 0.00 0.00 0.00 3.43
3870 4694 5.682659 TGGTAGTGCAAAAAGGTGTAAGTA 58.317 37.500 0.00 0.00 0.00 2.24
3944 4768 3.157087 CTCTTTGCTTGGTGGGTATTGT 58.843 45.455 0.00 0.00 0.00 2.71
3980 4804 3.630312 ACCGTCTAGCTTCTTCATCTCTC 59.370 47.826 0.00 0.00 0.00 3.20
4023 4847 5.996644 TCAACACAACTTTCTAAGGGAAGA 58.003 37.500 0.00 0.00 35.16 2.87
4060 4884 4.321899 GCATCCACAAAGATAAGGCAAACA 60.322 41.667 0.00 0.00 0.00 2.83
4123 5589 5.476599 TGTGCATGCTTTCTAAAACCACTAT 59.523 36.000 20.33 0.00 0.00 2.12
4189 5655 2.593148 AACGCACGGGCATTGTGA 60.593 55.556 11.77 0.00 39.73 3.58
4192 5658 1.992233 ATAGCAACGCACGGGCATTG 61.992 55.000 15.24 15.24 45.48 2.82
4195 5661 3.124270 CATAGCAACGCACGGGCA 61.124 61.111 11.77 0.00 41.24 5.36
4297 5766 2.352422 GCTCCCATGGTCACTGCA 59.648 61.111 11.73 0.00 0.00 4.41
4298 5767 2.042831 GTGCTCCCATGGTCACTGC 61.043 63.158 11.73 7.75 0.00 4.40
4362 5831 8.802267 CCAAATCTCCATTGTCCTAACTTTAAA 58.198 33.333 0.00 0.00 0.00 1.52
4363 5832 8.167392 TCCAAATCTCCATTGTCCTAACTTTAA 58.833 33.333 0.00 0.00 0.00 1.52
4364 5833 7.695055 TCCAAATCTCCATTGTCCTAACTTTA 58.305 34.615 0.00 0.00 0.00 1.85
4365 5834 6.552008 TCCAAATCTCCATTGTCCTAACTTT 58.448 36.000 0.00 0.00 0.00 2.66
4366 5835 6.139679 TCCAAATCTCCATTGTCCTAACTT 57.860 37.500 0.00 0.00 0.00 2.66
4367 5836 5.339530 CCTCCAAATCTCCATTGTCCTAACT 60.340 44.000 0.00 0.00 0.00 2.24
4368 5837 4.884164 CCTCCAAATCTCCATTGTCCTAAC 59.116 45.833 0.00 0.00 0.00 2.34
4369 5838 4.788075 TCCTCCAAATCTCCATTGTCCTAA 59.212 41.667 0.00 0.00 0.00 2.69
4370 5839 4.370776 TCCTCCAAATCTCCATTGTCCTA 58.629 43.478 0.00 0.00 0.00 2.94
4371 5840 3.192944 TCCTCCAAATCTCCATTGTCCT 58.807 45.455 0.00 0.00 0.00 3.85
4372 5841 3.054065 ACTCCTCCAAATCTCCATTGTCC 60.054 47.826 0.00 0.00 0.00 4.02
4373 5842 4.227864 ACTCCTCCAAATCTCCATTGTC 57.772 45.455 0.00 0.00 0.00 3.18
4374 5843 4.384647 GCTACTCCTCCAAATCTCCATTGT 60.385 45.833 0.00 0.00 0.00 2.71
4375 5844 4.133078 GCTACTCCTCCAAATCTCCATTG 58.867 47.826 0.00 0.00 0.00 2.82
4376 5845 3.782523 TGCTACTCCTCCAAATCTCCATT 59.217 43.478 0.00 0.00 0.00 3.16
4377 5846 3.387962 TGCTACTCCTCCAAATCTCCAT 58.612 45.455 0.00 0.00 0.00 3.41
4378 5847 2.768527 CTGCTACTCCTCCAAATCTCCA 59.231 50.000 0.00 0.00 0.00 3.86
4379 5848 2.769095 ACTGCTACTCCTCCAAATCTCC 59.231 50.000 0.00 0.00 0.00 3.71
4380 5849 3.490078 CGACTGCTACTCCTCCAAATCTC 60.490 52.174 0.00 0.00 0.00 2.75
4381 5850 2.428890 CGACTGCTACTCCTCCAAATCT 59.571 50.000 0.00 0.00 0.00 2.40
4382 5851 2.427453 TCGACTGCTACTCCTCCAAATC 59.573 50.000 0.00 0.00 0.00 2.17
4383 5852 2.457598 TCGACTGCTACTCCTCCAAAT 58.542 47.619 0.00 0.00 0.00 2.32
4384 5853 1.919240 TCGACTGCTACTCCTCCAAA 58.081 50.000 0.00 0.00 0.00 3.28
4385 5854 1.819288 CTTCGACTGCTACTCCTCCAA 59.181 52.381 0.00 0.00 0.00 3.53
4426 5939 0.840722 TCCTCCCCAGAAAGGTGTCC 60.841 60.000 0.00 0.00 34.12 4.02
4427 5940 0.615850 CTCCTCCCCAGAAAGGTGTC 59.384 60.000 0.00 0.00 34.12 3.67
4428 5941 1.492993 GCTCCTCCCCAGAAAGGTGT 61.493 60.000 0.00 0.00 34.12 4.16
4429 5942 1.301293 GCTCCTCCCCAGAAAGGTG 59.699 63.158 0.00 0.00 34.12 4.00
4430 5943 1.925972 GGCTCCTCCCCAGAAAGGT 60.926 63.158 0.00 0.00 34.12 3.50
4431 5944 3.002371 GGCTCCTCCCCAGAAAGG 58.998 66.667 0.00 0.00 37.03 3.11
4432 5945 2.586792 CGGCTCCTCCCCAGAAAG 59.413 66.667 0.00 0.00 0.00 2.62
4433 5946 3.717294 GCGGCTCCTCCCCAGAAA 61.717 66.667 0.00 0.00 0.00 2.52
4434 5947 4.722535 AGCGGCTCCTCCCCAGAA 62.723 66.667 0.00 0.00 0.00 3.02
4441 5954 4.087892 TTCCTGCAGCGGCTCCTC 62.088 66.667 8.66 0.00 41.91 3.71
4442 5955 4.093291 CTTCCTGCAGCGGCTCCT 62.093 66.667 8.66 0.00 41.91 3.69
4443 5956 3.612247 TTCTTCCTGCAGCGGCTCC 62.612 63.158 8.66 0.00 41.91 4.70
4444 5957 1.237285 TTTTCTTCCTGCAGCGGCTC 61.237 55.000 8.66 0.00 41.91 4.70
4445 5958 0.610232 ATTTTCTTCCTGCAGCGGCT 60.610 50.000 8.66 0.00 41.91 5.52
4446 5959 0.179153 GATTTTCTTCCTGCAGCGGC 60.179 55.000 8.66 0.31 41.68 6.53
4447 5960 0.453390 GGATTTTCTTCCTGCAGCGG 59.547 55.000 8.66 0.00 32.68 5.52
4528 6041 9.421806 TCATGTTTTGCATAGGAAAGTATTTTG 57.578 29.630 0.00 0.00 35.31 2.44
4539 6136 2.492881 TGCCACTCATGTTTTGCATAGG 59.507 45.455 0.00 0.00 35.74 2.57
4558 6155 4.980805 TCCAACGAGCCACCGTGC 62.981 66.667 0.00 0.00 42.54 5.34
4561 6158 4.308458 TGGTCCAACGAGCCACCG 62.308 66.667 0.00 0.00 35.55 4.94
4569 6166 0.905357 AGATCCCTTCTGGTCCAACG 59.095 55.000 0.00 0.00 31.79 4.10
4597 6194 1.152649 AATCCCCCTCATCCATCCAC 58.847 55.000 0.00 0.00 0.00 4.02
4641 6238 4.344865 GGTGGTGGTGGTGGCGAT 62.345 66.667 0.00 0.00 0.00 4.58
4657 6254 5.505780 TCTTATAATTGGAGTTGGTGGTGG 58.494 41.667 0.00 0.00 0.00 4.61
4658 6255 7.993183 ACTATCTTATAATTGGAGTTGGTGGTG 59.007 37.037 0.00 0.00 0.00 4.17
4659 6256 8.102484 ACTATCTTATAATTGGAGTTGGTGGT 57.898 34.615 0.00 0.00 0.00 4.16
4660 6257 9.712305 CTACTATCTTATAATTGGAGTTGGTGG 57.288 37.037 0.00 0.00 0.00 4.61
4709 6309 7.883833 TCTTCAGCACTCTTTTCTCTACTACTA 59.116 37.037 0.00 0.00 0.00 1.82
4710 6310 6.717540 TCTTCAGCACTCTTTTCTCTACTACT 59.282 38.462 0.00 0.00 0.00 2.57
4711 6311 6.915349 TCTTCAGCACTCTTTTCTCTACTAC 58.085 40.000 0.00 0.00 0.00 2.73
4806 6406 2.170187 CCATTCTGCAGAAGTAGGCTCT 59.830 50.000 31.14 11.79 37.48 4.09
4827 6431 7.269297 GCTTTTCTGTTATCAAGTTCATCGAAC 59.731 37.037 0.00 0.00 42.25 3.95
4848 6452 4.644685 ACAGTGTTGTCAAGGTATGCTTTT 59.355 37.500 0.00 0.00 29.46 2.27
4857 6461 2.287915 GTGCTGTACAGTGTTGTCAAGG 59.712 50.000 23.44 0.00 38.76 3.61
5032 6637 5.814188 TGACTCATGATGATGTCTAAGCAAC 59.186 40.000 18.75 0.83 30.91 4.17
5158 6764 4.082895 GCTCAAGCTTATATCAGCCAATGG 60.083 45.833 0.00 0.00 41.12 3.16
5377 6983 1.203050 AGGCCCATGCAACTGTAACTT 60.203 47.619 0.00 0.00 40.13 2.66
5413 7029 1.597663 AGCGTTTGTAACAGCAGACAC 59.402 47.619 0.00 0.00 34.79 3.67
5418 7034 3.435327 CCAGATTAGCGTTTGTAACAGCA 59.565 43.478 0.00 0.00 34.79 4.41
5425 7041 3.678056 TGAGTCCAGATTAGCGTTTGT 57.322 42.857 0.00 0.00 0.00 2.83
5596 7213 5.126707 AGGAAATACGGTACTGAACGAAGAT 59.873 40.000 9.17 0.00 0.00 2.40
5635 7252 1.532078 TCCAGACCACGTAGGCACA 60.532 57.895 0.00 0.00 43.14 4.57
5698 7315 3.868757 TGTTTCGAAGATCGTCCAGAT 57.131 42.857 2.90 0.00 41.35 2.90
5707 7324 4.320494 GCAGTTGATGGTTGTTTCGAAGAT 60.320 41.667 0.00 0.00 35.04 2.40
5805 7422 0.253347 TCTCCCCAGCTTCCAGGAAT 60.253 55.000 1.09 0.00 0.00 3.01
5843 7460 3.005684 TGGAAAAATTCATCGCTGCTTGT 59.994 39.130 0.00 0.00 0.00 3.16
5863 7480 6.665992 ATGGAATGAATTCATGGATCTTGG 57.334 37.500 21.39 0.00 38.53 3.61
6127 7820 7.905493 GGACGAAACATCAGATTTGAGAAATAC 59.095 37.037 0.00 0.00 36.61 1.89
6135 7828 3.438087 AGCTGGACGAAACATCAGATTTG 59.562 43.478 0.00 0.00 0.00 2.32
6149 7843 3.081804 AGGGAAAACATAAAGCTGGACG 58.918 45.455 0.00 0.00 0.00 4.79
6176 7870 6.545504 TTGTCTGAATCTACAACTTGAAGC 57.454 37.500 0.00 0.00 30.88 3.86
6270 7968 6.544197 TGTATTGCCAGAAGTTGAAACTGTTA 59.456 34.615 0.00 0.00 39.66 2.41
6294 7992 8.538039 CGCAAGTAGAACATATATATGCAGATG 58.462 37.037 20.46 12.18 37.19 2.90
6295 7993 8.640091 CGCAAGTAGAACATATATATGCAGAT 57.360 34.615 20.46 0.00 37.19 2.90
6345 8043 0.529992 GGAGATACAACCTTCGGGCG 60.530 60.000 0.00 0.00 39.10 6.13
6387 8085 0.584876 AAGAAACCGGCGAAAACTCG 59.415 50.000 9.30 0.00 0.00 4.18
6435 8133 2.279784 GCGCTCCGGGAAGATGAG 60.280 66.667 0.00 0.00 0.00 2.90
6451 8149 1.419107 GAAATCGACCCGGACTTCGC 61.419 60.000 0.73 0.00 37.59 4.70
6597 8299 5.188327 TGCTTGTACCGAATCTGATCTAG 57.812 43.478 0.00 0.00 0.00 2.43
6601 8303 4.745125 CGTAATGCTTGTACCGAATCTGAT 59.255 41.667 0.00 0.00 0.00 2.90
6615 8317 6.149633 GTCTGAATTTTGAACCGTAATGCTT 58.850 36.000 0.00 0.00 0.00 3.91
6655 8357 1.694150 CTCTCACTTTCACCAGTCCCA 59.306 52.381 0.00 0.00 0.00 4.37
6661 8363 4.982241 AATTCTCCTCTCACTTTCACCA 57.018 40.909 0.00 0.00 0.00 4.17
6663 8365 5.994668 ACAGAAATTCTCCTCTCACTTTCAC 59.005 40.000 0.00 0.00 0.00 3.18
6664 8366 6.179906 ACAGAAATTCTCCTCTCACTTTCA 57.820 37.500 0.00 0.00 0.00 2.69
6667 8369 5.815233 TGACAGAAATTCTCCTCTCACTT 57.185 39.130 0.00 0.00 0.00 3.16
6668 8370 6.371595 AATGACAGAAATTCTCCTCTCACT 57.628 37.500 0.00 0.00 0.00 3.41
6669 8371 7.446001 AAAATGACAGAAATTCTCCTCTCAC 57.554 36.000 0.00 0.00 0.00 3.51
6702 8404 1.065928 CCGCCGGTGAGCTTACTAG 59.934 63.158 18.79 3.41 0.00 2.57
6703 8405 3.072486 GCCGCCGGTGAGCTTACTA 62.072 63.158 18.79 0.00 0.00 1.82
6704 8406 4.452733 GCCGCCGGTGAGCTTACT 62.453 66.667 18.79 0.00 0.00 2.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.